optitype

Profile HLA alleles using paired-end DNA or RNA sequencing FASTQ files using OptiType

usage

nexus run --nf-workflow hla_typing_optitype.nf \
    -c nextflow.config \
    -w work/ \
    --samples_tsv_file samples.tsv \
    --output_dir results/ \
    --params_optitype "--dna"

Note

Nextflow config files are available here. Use the config file that matches your installed Nexus version (e.g. nexus_v0.2.0_nextflow_slurm.config).

parameters

parameter	description
--samples_tsv_file	TSV file with the following columns: ‘sample_id’, ‘fastq_file_1’, ‘fastq_file_2’.
--output_dir	Directory to which output files will be copied.
--params_optitype	OptiTypePipeline.py. parameters (default: ‘“--dna”’). Note that the parameters need to be wrapped in quotes and a space at the end of the string is necessary.